Basically I played my first ever mission since owning the game. Whilst I was retrieving a crate from inside a wrecked ship someone came along and destroyed my ship. What sort of gameplay mechanic is that?
There's a lot of asshatery going on out there right now, and an asshat found you. Just one of the joys of online gaming. I'm interested to see how some of the upcoming "law and order" mechanics will curb this behavior, if at all.
Then I have to wait 5 minutes for a new ship. How do I prevent that?
You can't, that's the insurance claim time to get a new one. At least you're not waiting 15 mins like I do whenever I lose my Cutlass! Even my Arrow is 7 minutes. You can pay extra credits to expedite the retrieval if you don't want to wait that long.
I also understand that someone could also steal my ship. Can a ship be left with the door shut and be impervious to theft?
No, you have to lock it via the context menu when you're in the cockpit. You'll see an option that says "Press to Lock" and "Press to Unlock." Click "Press to Lock" to lock your ship if you don't want anyone to steal it.
Then I had an issue using the quantum drive. It activated but the ship went nowhere. That could have been an error on my part,I'm not sure but I had been using it ok minutes earlier.
I've had that happen, so what I do is move my marker off the destination, move it back on then re-calibrate/spool. That's fixed it every single time so far. It could also be the cooldown time. Sometimes it shows for me, and sometimes it doesn't. The joys of a buggy "alpha"!